Atomic determinants for inducing β conformation in protein structure
کد مقاله : 1105-PHYSCHEM20
سیده بهاره شکری *
چکیده مقاله:
Statistical analysis on existing structural files of proteins indicates that 400 possible dipeptides are differently distributed in defined structural classes of proteins. We took 12 favorable dipeptides for beta conformation along with 12 dipeptides that are not significantly found in this conformation. The structures were geometrically optimized at DFT level (B3LYP 6-311++g**) and their physico chemical properties including bond lengths, bond angles, torsion angles and charge distribution on specific atoms were calculated by Gaussian 09 program. For mimicking the beta sheet secondary structure, in our peptide model; the φ and ψ torsion angles were constraint to β conformation. The output of the computational study was statistically compared using T-test analysis and it was found that the bond lengths of N-H and Cα1-C1 are significantly different in two datasets. It was also revealed that bond angles including C1-N1-H2 and H2-N2-Cα2 are different in two groups. However, there was no significant difference in specifying torsion angles for the planarity of peptide plane.
Concerning the importance of N-H group in forming the hydrogen bonds as well as dipole-dipole interaction in protein folding; it may be concluded that the peptide plane dictates its structural roles via its N-H moiety.
کلیدواژه ها:
Protein; Dipeptide; Conformation; DFT; Gaussian.
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